MolNFT v1 · #31614 · protein

Crystal structure of UPLC1 gap domain

2B0O: “Crystal structure of UPLC1 gap domain”. X-ray diffraction, 1 ligand (ZN), 16 pockets (best druggability 0.85). MolNFT v1 #31614 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2B0O
Type: protein
Length: 1,045 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: UPLC1
UniProt: Q6P9F4
Ligands: ZN
Pockets: 16 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 48% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	UPLC1	protein	264	46% helix, 6% strand	Q6P9F4
F	UPLC1	protein	266	48% helix, 5% strand	Q6P9F4
G	UPLC1	protein	253	51% helix, 5% strand	Q6P9F4
H	UPLC1	protein	262	46% helix, 5% strand	Q6P9F4

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains E, F, G, H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	918	0.85	0.87	76	empty
2	150	0.77	0.95	24	empty
3	675	0.74	0.80	57	empty
4	429	0.67	0.80	46	empty
5	200	0.67	0.85	26	empty

Interfaces

6 interfaces between chains.

E–F · 2448 Å² buried · 27 hydrogen bonds · protein-protein
G–H · 2266 Å² buried · 21 hydrogen bonds · protein-protein
E–G · 409 Å² buried · 3 hydrogen bonds · protein-protein
F–H · 344 Å² buried · 5 hydrogen bonds · protein-protein
F–G · 270 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2B0O · Crystal structure of UPLC1 GAP domain · the same entry in another collection · chain E against E, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q6P9F4
Elsewhere: RCSB PDB 2B0O · PDBe 2B0O · UniProt Q6P9F4

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